title: Expression profiling of chicken DT40 lymphoma cells indicates clonal selection of knockout and gene reconstituted cells.
abstract: The DT40 cell-line has been extensively used to create deletion mutants, one of which lacks Bruton's tyrosine kinase (Btk). Btk is a cytoplasmic tyrosine kinase important for B-lymphocyte maturation. It was previously shown that there are differences in gene expression between wild-type and Btk-deficient animals. Global gene expression profiling of the avian B-lymphoma DT40 cell-line was used as a model to differentiate among Btk knockout (KO) and Btk KO cells reconstituted with human Btk. Differences in the gene expression pattern showed statistically significant changes between parental DT40 and all the Btk KO cell populations irrespective of whether they are reconstituted or not. These results imply that in the process of generating a knockout cell-line, sub-clones are selected, which have multiple changes in their gene expression pattern (p<0.01). Although other parameters could also influence the expression profile, this potentially has important implications when interpreting microarray data from gene-deleted cell-lines.
authors.affiliation: Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, 14186 Huddinge, Stockholm, Sweden. Electronic address: hossain.nawaz@ki.se.
authors.forename: Hossain M
authors.initials: HM
authors.lastname: Nawaz
authors.affiliation: Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, 14186 Huddinge, Stockholm, Sweden.
authors.forename: K Emelie M
authors.initials: KEM
authors.lastname: Blomberg
authors.affiliation: Department of Informatics, University of Oslo, Oslo, Norway.
authors.forename: Jessica M
authors.initials: JM
authors.lastname: Lindvall
authors.affiliation: Laboratory for Lymphocyte Differentiation, RIKEN Research Center for Allergy and Immunology, Tsurumi-ku, Yokohama, Kanagawa 230-0045, Japan.
authors.forename: Tomohiro
authors.initials: T
authors.lastname: Kurosaki
authors.affiliation: Clinical Research Center, Department of Laboratory Medicine, Karolinska Institutet, Karolinska University Hospital Huddinge, 14186 Huddinge, Stockholm, Sweden. Electronic address: edvard.smith@ki.se.
authors.forename: C I Edvard
authors.initials: CIE
authors.lastname: Smith
mesh_terms: D000077329:Agammaglobulinaemia Tyrosine Kinase; D000818:Animals; D045744:Cell Line, Tumor; D002645:Chickens; D002999:Clone Cells; D020869:Gene Expression Profiling; D055786:Gene Knockout Techniques; D006801:Humans; D016393:Lymphoma, B-Cell / Q000235:genetics*; D009154:Mutation; D011505:Protein-Tyrosine Kinases / Q000235:genetics*
chemical_list: D011505:Protein-Tyrosine Kinases; D000077329:Agammaglobulinaemia Tyrosine Kinase; C000625949:BTK protein, human